🧬 Topic 6: Detailed Solutions

Nucleic Acids (Нуклеиновые кислоты)
Problem 1: Complete Acidic Hydrolysis of Adenosine 5'-monophosphate (AMP)
📋 Task:

Write the reaction of the complete acidic hydrolysis of adenosine 5'-monophosphate (AMP, 5'-adenylic acid). Name all products. What nucleic acid can contain the given nucleotide?

AMP Structure and Hydrolysis
AMP Components:
  • Nitrogenous base: Adenine (purine)
  • Sugar: D-Ribose (pentose)
  • Phosphate: One phosphate group at 5' position

📦 AMP Structure:

Adenosine 5'-monophosphate (AMP)
Complete Acidic Hydrolysis:

AMP + 2H₂O + H⁺ → Adenine + D-Ribose + Phosphoric acid

Bonds broken:
• N-glycosidic bond (between adenine N9 and ribose C1')
• Phosphoester bond (between ribose C5' and phosphate)
Adenine
D-Ribose
Phosphoric Acid
Hydrolysis Products:
• Adenine (6-aminopurine)
• D-Ribose (pentose sugar)
• Phosphoric acid (H₃PO₄)

Nucleic Acid: RNA (Ribonucleic acid)
Reason: AMP contains ribose (not deoxyribose), found in RNA
Biological Importance of AMP:
  • RNA building block: One of 4 ribonucleotides in RNA
  • Energy metabolism: Precursor to ADP and ATP
  • Signaling: Component of cAMP (second messenger)
  • Enzyme regulation: Allosteric regulator
Problem 2: Complete Acidic Hydrolysis of Thymidine 3'-monophosphate (TMP)
📋 Task:

Write the reaction of the complete acidic hydrolysis of thymidine 3'-monophosphate (TMP, 3'-thymidylic acid). Name all products.

TMP Structure and Hydrolysis
TMP Components:
  • Nitrogenous base: Thymine (pyrimidine)
  • Sugar: 2'-Deoxy-D-ribose (pentose without 2'-OH)
  • Phosphate: One phosphate group at 3' position

📦 TMP Structure:

Thymidine 3'-monophosphate (TMP)
Complete Acidic Hydrolysis:

TMP + 2H₂O + H⁺ → Thymine + 2'-Deoxy-D-ribose + Phosphoric acid

Bonds broken:
• N-glycosidic bond (between thymine N1 and deoxyribose C1')
• Phosphoester bond (between deoxyribose C3' and phosphate)
Thymine
2'-Deoxy-D-ribose
Phosphoric Acid
Hydrolysis Products:
• Thymine (5-methyluracil)
• 2'-Deoxy-D-ribose (deoxyribose sugar)
• Phosphoric acid (H₃PO₄)

Nucleic Acid: DNA (Deoxyribonucleic acid)
Reason: TMP contains deoxyribose and thymine, found only in DNA
Biological Importance of TMP:
  • DNA building block: One of 4 deoxyribonucleotides in DNA
  • Base pairing: Pairs with adenine (2 H-bonds)
  • DNA synthesis: Incorporated as dTTP during replication
  • Unique to DNA: Thymine not found in RNA (replaced by uracil)
Problem 3: RNA Dinucleotide Formation (UMP + CMP)
📋 Task:

Write the reaction between uridine 5'-monophosphate and cytidine 5'-monophosphate occurred in RNA synthesis. Name all types of bond in the product.

RNA Dinucleotide Synthesis
Components:
  • UMP: Uridine 5'-monophosphate (uracil + ribose + phosphate)
  • CMP: Cytidine 5'-monophosphate (cytosine + ribose + phosphate)
  • Bond formed: 3',5'-phosphodiester bond
Condensation Reaction:

UMP (5') + CMP (5') → UpC + PPi (or H₂O in simplified form)

Structure:
Uracil-Ribose-O-P(O)₂-O-Ribose-Cytosine
(5') (3')
UMP
CMP
UpC Dinucleotide (RNA)

Types of Bonds in RNA Dinucleotide:

  1. Phosphodiester bond: Between 3'-OH of UMP ribose and 5'-phosphate of CMP (3',5'-linkage)
  2. N-glycosidic bonds: Between base N and ribose C1' (2 bonds: uracil N1-C1' and cytosine N1-C1')
  3. Phosphoester bonds: Between ribose C5' and phosphate (in each nucleotide)
  4. Covalent bonds in bases: C-C, C-N, C=O, C-H, N-H within uracil and cytosine
  5. Covalent bonds in ribose: C-C, C-O, C-H, O-H within sugar rings
Product: Uridylyl-(3'→5')-cytidine or UpC
Bond Types:
• 1 × 3',5'-phosphodiester bond (links nucleotides)
• 2 × N-glycosidic bonds (base-sugar)
• 2 × Phosphoester bonds (sugar-phosphate)
• Multiple covalent bonds within bases and sugars

Direction: 5'→3' (UMP at 5' end, CMP at 3' end)
RNA Synthesis (Transcription):
  • Enzyme: RNA polymerase
  • Template: DNA strand
  • Direction: 5'→3' synthesis
  • Energy: Nucleoside triphosphates (NTPs) provide energy
  • Leaving group: Pyrophosphate (PPi)
Problem 4: DNA Dinucleotide Formation (dTMP + dGMP)
📋 Task:

Write the reaction between thymidine 5'-monophosphate and deoxyguanosine 5'-monophosphate occurred in DNA synthesis. Name all types of bond in the product.

DNA Dinucleotide Synthesis
Components:
  • dTMP: Deoxythymidine 5'-monophosphate (thymine + deoxyribose + phosphate)
  • dGMP: Deoxyguanosine 5'-monophosphate (guanine + deoxyribose + phosphate)
  • Bond formed: 3',5'-phosphodiester bond
Condensation Reaction:

dTMP (5') + dGMP (5') → dTpG + PPi (or H₂O in simplified form)

Structure:
Thymine-Deoxyribose-O-P(O)₂-O-Deoxyribose-Guanine
(5') (3')
dTMP
dGMP
dTpG Dinucleotide (DNA)

Types of Bonds in DNA Dinucleotide:

  1. Phosphodiester bond: Between 3'-OH of dTMP deoxyribose and 5'-phosphate of dGMP
  2. N-glycosidic bonds: Thymine N1-C1' and Guanine N9-C1'
  3. Phosphoester bonds: Between deoxyribose C5' and phosphate
  4. Key difference from RNA: Deoxyribose lacks 2'-OH group (only 2'-H)
Product: Deoxythymidylyl-(3'→5')-deoxyguanosine or dTpG
Bond Types:
• 1 × 3',5'-phosphodiester bond
• 2 × N-glycosidic bonds
• 2 × Phosphoester bonds
• Multiple covalent bonds within bases and deoxyribose sugars

Direction: 5'→3' (dTMP at 5' end, dGMP at 3' end)
DNA Synthesis (Replication):
  • Enzyme: DNA polymerase
  • Template: Parent DNA strand
  • Direction: 5'→3' synthesis
  • Energy: Deoxynucleoside triphosphates (dNTPs)
  • Proofreading: 3'→5' exonuclease activity
  • Base pairing: T pairs with A (2 H-bonds), G pairs with C (3 H-bonds)
Problem 5: DNA Sequence 5'-C T G-3' with Complementary Triplet
📋 Task:

Draw the DNA sequence 5'-C T G-3'. For the given sequence draw the complimentary triplet. Show all hydrogen bonds between complimentary nucleic bases.

DNA Base Pairing
5' - C - T - G - 3'
|||    ||    |||
3' - G - A - C - 5'
Base Pairing Rules (Chargaff's Rules):
⬇
Cytosine (C) ⟷ Guanine (G): 3 Hydrogen Bonds
Thymine (T) ⟷ Adenine (A): 2 Hydrogen Bonds
Guanine (G) ⟷ Cytosine (C): 3 Hydrogen Bonds
C-G Base Pair
3 H-bonds
T-A Base Pair
2 H-bonds
G-C Base Pair
3 H-bonds

Hydrogen Bond Details:

  1. C-G pair (3 H-bonds):
    • N4-H···O6 (cytosine to guanine)
    • N3···H-N1 (cytosine to guanine)
    • O2···H-N2 (cytosine to guanine)
  2. T-A pair (2 H-bonds):
    • N3-H···N1 (thymine to adenine)
    • O4···H-N6 (thymine to adenine)
  3. Antiparallel: Strands run in opposite directions (5'→3' and 3'→5')
Original Sequence: 5'-C T G-3'
Complementary Sequence: 3'-G A C-5'
Total Hydrogen Bonds: 3 + 2 + 3 = 8 H-bonds
Orientation: Antiparallel (opposite directions)
Biological Significance:
  • DNA stability: G-C pairs (3 H-bonds) more stable than A-T pairs (2 H-bonds)
  • Melting temperature: Higher G-C content = higher Tm
  • Replication fidelity: Complementary base pairing ensures accurate copying
  • Double helix: H-bonds hold two strands together
Problem 6: RNA Sequence 5'-A G U-3' with Complementary Triplet
📋 Task:

Draw the RNA sequence 5'-A G U-3'. For the given sequence draw the complimentary triplet. Show all hydrogen bonds between complimentary nucleic bases.

RNA Base Pairing
5' - A - G - U - 3'
||    |||    ||
3' - U - C - A - 5'
RNA Base Pairing Rules:
⬇
Adenine (A) ⟷ Uracil (U): 2 Hydrogen Bonds
Guanine (G) ⟷ Cytosine (C): 3 Hydrogen Bonds
Uracil (U) ⟷ Adenine (A): 2 Hydrogen Bonds
A-U Base Pair
2 H-bonds (RNA)
G-C Base Pair
3 H-bonds
U-A Base Pair
2 H-bonds (RNA)
Problem 7: Complete Acidic Hydrolysis of Guanosine 5'-monophosphate (GMP)
📋 Task:

Write the reaction of the complete acidic hydrolysis of guanosine 5'-monophosphate (GMP, 5'-guanylic acid). Name all products. What nucleic acid can contain the given nucleotide?

GMP Structure and Hydrolysis
GMP Components:
  • Nitrogenous base: Guanine (purine)
  • Sugar: D-Ribose (pentose)
  • Phosphate: One phosphate group at 5' position

📦 GMP Structure:

Guanosine 5'-monophosphate (GMP)
Complete Acidic Hydrolysis:

GMP + 2H₂O + H⁺ → Guanine + D-Ribose + Phosphoric acid

Bonds broken:
• N-glycosidic bond (between guanine N9 and ribose C1')
• Phosphoester bond (between ribose C5' and phosphate)
Guanine
D-Ribose
Phosphoric Acid
Hydrolysis Products:
• Guanine (2-amino-6-oxopurine)
• D-Ribose (pentose sugar)
• Phosphoric acid (H₃PO₄)

Nucleic Acid: RNA (Ribonucleic acid)
Reason: GMP contains ribose, found in RNA
Biological Importance of GMP:
  • RNA building block: One of 4 ribonucleotides in RNA
  • Base pairing: Pairs with cytosine (3 H-bonds)
  • Signaling: Component of cGMP (second messenger)
  • Energy metabolism: Precursor to GDP and GTP
Problem 8: Complete Acidic Hydrolysis of Deoxycytidine 5'-monophosphate (dCMP)
📋 Task:

Write the reaction of the complete acidic hydrolysis of deoxycytidine 5'-monophosphate (dCMP). Name all products. What nucleic acid can contain the given nucleotide?

dCMP Structure and Hydrolysis
dCMP Components:
  • Nitrogenous base: Cytosine (pyrimidine)
  • Sugar: 2'-Deoxy-D-ribose
  • Phosphate: One phosphate group at 5' position

📦 dCMP Structure:

Deoxycytidine 5'-monophosphate (dCMP)
Complete Acidic Hydrolysis:

dCMP + 2H₂O + H⁺ → Cytosine + 2'-Deoxy-D-ribose + Phosphoric acid

Bonds broken:
• N-glycosidic bond (between cytosine N1 and deoxyribose C1')
• Phosphoester bond (between deoxyribose C5' and phosphate)
Cytosine
2'-Deoxy-D-ribose
Phosphoric Acid
Hydrolysis Products:
• Cytosine (4-amino-2-oxopyrimidine)
• 2'-Deoxy-D-ribose
• Phosphoric acid (H₃PO₄)

Nucleic Acid: DNA (Deoxyribonucleic acid)
Reason: dCMP contains deoxyribose, found in DNA
Biological Importance of dCMP:
  • DNA building block: One of 4 deoxyribonucleotides in DNA
  • Base pairing: Pairs with guanine (3 H-bonds)
  • DNA synthesis: Incorporated as dCTP during replication
  • Methylation: Can be methylated to form 5-methylcytosine (epigenetic marker)
Problem 9: ATP Structure and Hydrolysis to ADP
📋 Task:

Draw the structure of adenosine triphosphate (ATP). Write the reaction of ATP hydrolysis to ADP. Calculate the energy released. Name all types of bonds in ATP.

ATP Structure and Energy Release
ATP Components:
  • Nitrogenous base: Adenine
  • Sugar: D-Ribose
  • Phosphates: Three phosphate groups (α, β, γ)

📦 ATP Structure:

Adenosine Triphosphate (ATP)
ATP Hydrolysis:

ATP + H₂O → ADP + Pi + Energy

Energy released:
ΔG°' = -30.5 kJ/mol (-7.3 kcal/mol)

Bond broken:
Phosphoanhydride bond between β and γ phosphates

Types of Bonds in ATP:

  1. N-glycosidic bond: Between adenine N9 and ribose C1'
  2. Phosphoester bond: Between ribose C5' and α-phosphate (stable)
  3. Phosphoanhydride bonds: Between α-β and β-γ phosphates (high-energy)
  4. High-energy bonds: Phosphoanhydride bonds release ~30.5 kJ/mol when hydrolyzed
Products: ADP (adenosine diphosphate) + Inorganic phosphate (Pi)
Energy released: -30.5 kJ/mol
Bond Types:
• 1 × N-glycosidic bond
• 1 × Phosphoester bond
• 2 × Phosphoanhydride bonds (high-energy)
Biological Importance of ATP:
  • Energy currency: Universal energy carrier in cells
  • Phosphate donor: For phosphorylation reactions
  • Active transport: Powers ion pumps (Na⁺/K ATPase)
  • Muscle contraction: Provides energy for myosin
  • Biosynthesis: Drives endergonic reactions
Problem 10: Cyclic AMP (cAMP) Formation from ATP
📋 Task:

Write the reaction of cyclic AMP (cAMP) formation from ATP. Draw the structure of cAMP. Explain its biological role as a second messenger.

cAMP Formation and Function
Reaction:
  • Enzyme: Adenylate cyclase
  • Substrate: ATP
  • Product: cAMP + PPi (pyrophosphate)
  • Bond formed: 3',5'-cyclic phosphodiester bond
cAMP Formation:

ATP → cAMP + PPi

Mechanism:
Intramolecular cyclization: 3'-OH attacks α-phosphate
Forms 3',5'-cyclic phosphodiester bond
ATP
Cyclic AMP (cAMP)

Structural Features of cAMP:

  1. Cyclic structure: Phosphate forms bridge between C3' and C5' of ribose
  2. 3',5'-cyclic phosphodiester: Unique cyclic bond
  3. Adenine base: Unchanged from ATP
  4. Second messenger: Intracellular signaling molecule
Product: Adenosine 3',5'-cyclic monophosphate (cAMP)
Enzyme: Adenylate cyclase
Bond formed: 3',5'-cyclic phosphodiester bond
Byproduct: Pyrophosphate (PPi)
cAMP as Second Messenger:
  • Signal transduction: Hormone (1st messenger) → cAMP (2nd messenger)
  • Protein Kinase A: cAMP activates PKA
  • Glycogen metabolism: Stimulates glycogen breakdown
  • Gene expression: Regulates transcription via CREB
  • Heart function: β-adrenergic signaling
  • Termination: Degraded by phosphodiesterase to AMP
Problem 11: RNA Tetranucleotide Formation (ApGpCpU)
📋 Task:

Write the reaction for formation of RNA tetranucleotide 5'-A-G-C-U-3' from mononucleotides. Name all phosphodiester bonds. Calculate total number of bonds formed.

RNA Tetranucleotide Synthesis
Components:
  • AMP: Adenosine 5'-monophosphate
  • GMP: Guanosine 5'-monophosphate
  • CMP: Cytidine 5'-monophosphate
  • UMP: Uridine 5'-monophosphate
Overall Reaction:

AMP + GMP + CMP + UMP → ApGpCpU + 3H₂O

Stepwise formation:
Step 1: AMP + GMP → ApG + H₂O
Step 2: ApG + CMP → ApGpC + H₂O
Step 3: ApGpC + UMP → ApGpCpU + H₂O

Direction: 5'→3' synthesis
RNA Tetranucleotide: 5'-ApGpCpU-3'
5'-A-G-C-U-3' (4 nucleotides, 3 phosphodiester bonds)

Bond Analysis:

  1. Phosphodiester bonds formed: 3 bonds
    • Bond 1: A(3')-O-P-O-G(5')
    • Bond 2: G(3')-O-P-O-C(5')
    • Bond 3: C(3')-O-P-O-U(5')
  2. Water molecules released: 3 H₂O
  3. Total covalent bonds in product:
    • 3 × phosphodiester bonds
    • 4 × N-glycosidic bonds
    • 4 × phosphoester bonds (at 5' ends)

Hydrogen Bond Details (RNA):

  1. A-U pair (2 H-bonds):
    • N6-H···O4 (adenine to uracil)
    • N1···H-N3 (adenine to uracil)
  2. G-C pair (3 H-bonds): Same as DNA
  3. Key difference from DNA: Uracil instead of Thymine (no 5-methyl group)
  4. RNA structure: Usually single-stranded but can form double-stranded regions
Original Sequence: 5'-A G U-3'
Complementary Sequence: 3'-U C A-5'
Total Hydrogen Bonds: 2 + 3 + 2 = 7 H-bonds
Orientation: Antiparallel
RNA-specific: Uracil instead of Thymine
RNA vs DNA Base Pairing:
  • Uracil vs Thymine: U pairs with A (like T in DNA)
  • RNA structures: Hairpins, stem-loops, internal loops
  • mRNA: Carries genetic code from DNA to ribosome
  • tRNA: Brings amino acids during translation
  • rRNA: Component of ribosomes
  • Codons: 3-base sequences code for amino acids

End of Topic 6 Solutions

All nucleic acid structures, reactions, and base pairing covered with molecular visualizations.